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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Hi Emmanuel<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Calibrate your data on phantom to express it in photon fluence rate (photons * mm^-2 * s^2) or use differential data.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Please refer to vast literature on tomographic reconstruction and perturbation theory. Bioluminescence or NIRS, it does not matter, as the mechanism is all the same. A good start would be:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#1<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Durduran 2010, Diffuse optics for tissue monitoring and tomography<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>#2<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Dehghani 2008, Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Regards<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Stanislaw Wojtkiewicz, PhD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>---<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>School of Computer Science<o:p></o:p></span></p><p class=MsoNormal><span lang=PL style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>University of Birmingham<o:p></o:p></span></p><p class=MsoNormal><span lang=PL style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>B15 2TT<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> emmanuel.cosnard@outlook.fr <emmanuel.cosnard@outlook.fr> <br><b>Sent:</b> 20 March 2019 10:11<br><b>To:</b> nirfast@public.kitware.com; s.wojtkiewicz@cs.bham.ac.uk<br><b>Subject:</b> RE: [Nirfast] Normalisation of the measurements?<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Hello Stanislas,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you for taking the time to answer and sorry for my mistake, I am using <i>CSCGNW</i> bioluminescence, and the field I am referring to in NIRFAST is actually data_fn in the reconstruct_fl function. <o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'>function [fwd_mesh,pj_error] = reconstruct_fl(fwd_mesh,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> recon_basis,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> frequency,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> data_fn,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> iteration,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> lambda,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> output_fn,...</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><p class=MsoNormal><i><span style='font-family:"Calibri",sans-serif;color:black'> filter_n)</span></i><span style='font-family:"Calibri",sans-serif;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>data_fn are the boundery data measured, and I wanted to know if we have to normalise these data in a specific way.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you and regards,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Emmanuel<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div class=MsoNormal align=center style='text-align:center'><hr size=2 width="98%" align=center></div><div id=divRplyFwdMsg><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>De :</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> Stanislaw Wojtkiewicz <s.wojtkiewicz@cs.bham.ac.uk><br><b>Envoyé :</b> mercredi 20 mars 2019 10:01<br><b>À :</b> emmanuel.cosnard@outlook.fr; nirfast@public.kitware.com<br><b>Objet :</b> RE: [Nirfast] Normalisation of the measurements?</span> <o:p></o:p></p><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Emmanuel</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>It looks like the ‘</span><i><span style='font-family:"Calibri",sans-serif;color:black'>CSCGNW</span></i><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>’ function does not exist in NIRFAST.</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Even Google knows nothing about it:)</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Please, track down to whom this function belongs to.</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Also, regardless of the existence of the function, I have a strong impression that the current question might be outside of the scope of this mailing list….</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><div><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Regards</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Stanislaw Wojtkiewicz, PhD</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>---</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>School of Computer Science</span><o:p></o:p></p><p class=xmsonormal><span lang=PL style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>University of Birmingham</span><o:p></o:p></p><p class=xmsonormal><span lang=PL style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>B15 2TT</span><o:p></o:p></p></div><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=xmsonormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> emmanuel.cosnard@outlook.fr <emmanuel.cosnard@outlook.fr> <br><b>Sent:</b> 20 March 2019 09:36<br><b>To:</b> nirfast@public.kitware.com<br><b>Subject:</b> [Nirfast] Normalisation of the measurements?</span><o:p></o:p></p></div></div><p class=xmsonormal> <o:p></o:p></p><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Hello,</span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>I would like to know if we have to normalise our fluorescence measurements data in a specific way for the "measurements" vector transmitted in the CSCGNW function (<i>function [xFinal varargout] = CSCGNW(jacobianMatrix, measurements, recParam)</i>). </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>How do we take into account the time of exposure? Do the measures have to be between a specific range, or do we have to apply a specific function on it?</span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you and regards,</span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Emmanuel</span><o:p></o:p></p></div></div><div id="x_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div class=MsoNormal align=center style='text-align:center'><hr size=1 width="99%" noshade style='color:#909090' align=center></div><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 style='border-collapse:collapse'><tr><td style='padding:0cm 11.25pt 0cm 6.0pt'><p class=MsoNormal><a href="https://www.avast.com/antivirus"><span style='border:solid windowtext 1.0pt;padding:0cm;text-decoration:none'><img border=0 width=100 height=100 style='width:1.0416in;height:1.0416in' id="_x0000_i1027" src="cid:~WRD000.jpg" alt="Image removed by sender. Avast logo"></span></a><o:p></o:p></p></td><td style='padding:.75pt .75pt .75pt .75pt'><p><span style='font-family:"Calibri",sans-serif;color:#3D4D5A'>This email has been checked for viruses by Avast antivirus software. <br><a href="https://www.avast.com/antivirus">www.avast.com</a> <o:p></o:p></span></p></td></tr></table><p class=MsoNormal><br><br><o:p></o:p></p></div></div></div></body></html>